Metagenomic characterization of a novel non-ammonia-oxidizing Thaumarchaeota from hadal sediment

Background The hadal sediment, found at an ocean depth of more than 6000 m, is geographically isolated and under extremely high hydrostatic pressure, resulting in a unique ecosystem. Thaumarchaeota are ubiquitous marine microorganisms predominantly present in hadal environments. While there have been several studies on Thaumarchaeota there, most of them have primarily focused on ammonia-oxidizing archaea (AOA). However, systematic metagenomic research specifically targeting heterotrophic non-AOA Thaumarchaeota is lacking. Results In this study, we explored the metagenomes of Challenger Deep hadal sediment, focusing on the Thaumarchaeota. Functional analysis of sequence reads revealed the potential contribution of Thaumarchaeota to recalcitrant dissolved organic matter degradation. Metagenome assembly binned one new group of hadal sediment-specific and ubiquitously distributed non-AOA Thaumarchaeota, named Group-3.unk. Pathway reconstruction of this new type of Thaumarchaeota also supports heterotrophic characteristics of Group-3.unk, along with ABC transporters for the uptake of amino acids and carbohydrates and catabolic utilization of these substrates. This new clade of Thaumarchaeota also contains aerobic oxidation of carbon monoxide-related genes. Complete glyoxylate cycle is a distinctive feature of this clade in supplying intermediates of anabolic pathways. The pan-genomic and metabolic analyses of metagenome-assembled genomes belonging to Group-3.unk Thaumarchaeota have highlighted distinctions, including the dihydroxy phthalate decarboxylase gene associated with the degradation of aromatic compounds and the absence of genes related to the synthesis of some types of vitamins compared to AOA. Notably, Group-3.unk shares a common feature with deep ocean AOA, characterized by their high hydrostatic pressure resistance, potentially associated with the presence of V-type ATP and di-myo-inositol phosphate syntheses-related genes. The enrichment of organic matter in hadal sediments might be attributed to the high recruitment of sequence reads of the Group-3.unk clade of heterotrophic Thaumarchaeota in the trench sediment. Evolutionary and genetic dynamic analyses suggest that Group-3 non-AOA consists of mesophilic Thaumarchaeota organisms. These results indicate a potential role in the transition from non-AOA to AOA Thaumarchaeota and from thermophilic to mesophilic Thaumarchaeota, shedding light on recent evolutionary pathways. Conclusions One novel clade of heterotrophic non-AOA Thaumarchaeota was identified through metagenome analysis of sediments from Challenger Deep. Our study provides insight into the ecology and genomic characteristics of the new sub-group of heterotrophic non-AOA Thaumarchaeota, thereby extending the knowledge of the evolution of Thaumarchaeota. Video Abstract Supplementary Information The online version contains supplementary material available at 10.1186/s40168-023-01728-2.


Fig. S2
Fig. S2 Contig composition-independent profile of the assembled metagenome from Challenger Deep sediments.Circles represent contigs in the assembled metagenome of the MT1 sample, scaled by the square root of their length.Only contigs ≥ 5 kbp are shown.Circles are colored according to the taxonomy annotation by GTDB-Tk.

Fig. S3
Fig. S3 Average nucleotide identity (ANI) of Group-3.unkThaumarchaeota.MT1_thaum1 and MT7_thaum2 are metagenome-assembled genomes (MAGs) from this study.MT1_thaum1 and MT7_thaum2 have high similarity to Candidatus_Nitrosopumilus_sp_MTA1, which was binned from Mariana Trench water samples obtained at a depth of 8000 m in a previous study (1).MT1_thaum1 and other four related MAGs reconstructed from public metagenomic datasets in Group-3.unkshowed high ANI value (> 0.82) with intra-group comparison but low ANI value (< 0.73) with MAGs of other groups.

Fig. S5
Fig. S5 Phylogenetic tree and sequence alignment of aerobic carbon monoxide dehydrogenase large subunit (CoxL) amino acid sequences.Reference sequences of Forms I and II of CoxL were selected from published papers (2) and (3-5), respectively.Nodes with bootstrap values ≥ 60 are indicated.Motif sequences of active-site configurations are indicated with asterisks.Labels in red show the MT1_thaum1 genome.All Group-3.unkmembers possess the CoxL.Lineages marked in purple and blue indicate Forms I and II CoxL, respectively.

Fig. S6
Fig. S6 Orthologous gene analysis based on the evolution of Thaumarchaeota.A Principal coordinate analysis (PCoA) plot with Jaccard distance based on orthologous groups of genes in 81 selected genomes.PCoA of axes 1 vs. 2, 1 vs. 3, and 2 vs. 3 are shown.Colors represent different taxonomic groups.B Identified Clusters of Orthologous Gene (COG) functions of the gained and lost gene families of the corresponding evolutionary events.The node number is matched to the phylogenetic tree in Fig. 6.The functions of COG categories are as follows: C: energy production and conversion; D: cell cycle control, cell division, and chromosome partitioning; E: amino acid transport and metabolism; F: nucleotide transport and metabolism; G: carbohydrate transport and metabolism; H: coenzyme transport and metabolism; I: lipid transport and metabolism; J: translation, ribosomal structure, and biogenesis; K: transcription; L: replication, recombination, and repair; M: cell wall/membrane/envelope biogenesis; N: cell motility; O: post-translational modification and protein turnover; P: inorganic ion transport and metabolism; Q: secondary metabolites biosynthesis, transport, and catabolism; S: function unknown; T: signal transduction mechanisms; U: intracellular trafficking, secretion, and vesicular transport; V: defense mechanisms.

Fig. S7
Fig. S7 Optimal growth temperature (OGT) prediction of Aigarchaeota and Thaumarchaeota groups.Aigarchaeota and Group-1 Thaumarchaeota, which are mostly found in hot springs, exhibit a high OGT.AOA and other non-AOA Thaumarchaeota have a similar relatively low OGT.

Fig. S8
Fig. S8 Timing estimation analysis of Thaumarchaeota.The tree added 21 Euryarchaeota, 16 Crenarchaeota, one Korarchaeota, two Bathyarchaeota, and two DPANN archaea (as outgroup).Divergence nodes used for calibration are marked.Time unit at the bottom is millions of years (Ma).